The multiple sequence editor SeqPup has the ability to interface
with other programs like those of the Phylip package, and to
allow you to select subsets of your sequence alignment to send
to Phylip's app for processing.
At present you can only select contiguous subsets of your alignment
for this. I will plan to add the ability to mark non-contigous
regions in your alignment that can be selected for processing
by Phylip's and other programs.
Find SeqPup at ftp://iubio.bio.indiana.edu/molbio/seqpup/.
It works on Mac, MSWin, XWin.
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu